Wednesday, December 30, 2009

How Long Does It Take to Recognize an IDiot?


Ken Ham is the man behind Answers in Genesis and the Creation Museum. He's upset with Lawrence Krauss because Krauss has been critical of anti-science creationists in general and the Creation Museum in particular. Ken Ham is particularly upset because Krauss was critical of th Creation Museum before he had actually visited it.
Krauss himself got criticism from some in the secular press because he had not even visited the museum to see it for himself. Presumably because of this criticism, he did come some time later and walked through the Creation Museum exhibits with AiG’s CCO, Mark Looy. Mark actually timed Krauss’s visit. He took a whole 22 minutes to walk through the museum, most of the time asking Mark Looy questions and only occasionally glancing at some of the exhibits. Considering it would take a person nearly one and a half hours to watch the programs in the various theatres, including the Planetarium and SFX theatre, plus take 2 hours to watch all the 50-plus videos in the various exhibits, and a further two hours to read all the signage—it was obvious Krauss wasn’t the least bit interested in researching the content of the museum (as one would expect from a real scientist and well-known anti-creationist commentator), but only visited presumably to tell people he has seen the Creation Museum and thus could comment on it—what a farce!
Now, let's be fair to Lawrence Krauss. He's a very smart guy and I'm certain that it didn't take him 22 minutes to recognize that the museum was a farce. I'm sure he stayed an extra 21 minutes just to be polite to his host.



Thursday, December 17, 2009

Time Magazine's Top 10 Scientific Discoveries


Here's the list of Time Magazine's Top 10 Scientific Discoveries. Given all the hype about The Darwinius Affair last May it's amazing that the discovery of this fossil didn't make the list.

There were several other huge scientific breakthroughs that failed to make the list: proof that Darwin was wrong, the overthrow of evolutionary theory, exposing the fraud of climate change, and the publication of Unscientific America.

There are some real scientific stories that were ignored by Time magazine: the creation of artificial stem cells (continuing), the 150th anniversary of the publication of Origin of Species, Nobel Prizes for telomeres and ribosome structure, and rapid human genome sequencing.

1. Our Oldest Ancestor, "Ardi"
2. The Human Epigenome, Decoded
3. Gene Therapy Cures Color Blindness
4. A Robot Performs Science
5. Breeding Tuna on Land
6. Water on the Moon
7. The Fundamental Lemma, Solved
8. Teleportation!
9. The Large Hadron Collider, Revived
10. A New Planet (or Brown Dwarf?) Discovered

It looks like a bad year for science if this is the best of the best.

In case you've forgotten, here's the top 10 list from last year [2008].

1. Large Hadron Collider
2. The North Pole — of Mars
3. Creating Life
4. China Soars into Space
5. More Gorillas in the Mist
6. Brave New Worlds
7. The Power of Invisibility
8. Cenozoic Park?
9. Can You Spell Science?
10. First Family


Tuesday, December 15, 2009

Does Excess Genomic DNA Protect Against Mutation?

Many eukaryotic genomes have a large amount of "excess" DNA that doesn't have any of the functions we normally assign to DNA (protein-coding, regulatory, origins of replication, centromeres, RNA genes etc.). Many of us think this is junk DNA. It has no function and could easily be dispensed with.

One of the adaptive explanations for this excess DNA is that it protects the functional DNA from mutations. Ryan Gregory thinks this is a serious scientific hypothesis even though he's skeptical. He has a wonderful post that reviews the history of the idea and how the hypothesis should be tested [Does junk DNA protect against mutation?].

The bottom line is that this hypothesis is not taken very seriously by the scientific community for some very good reasons.

First, most spontaneous mutations in the germ line seem to be due to errors in DNA replication. The overall rate of evolutionary change is consistent with the mutation rate of DNA replication + repair, suggesting that it is the dominant form of mutation. This mutation rate is based on the number of nucleotides replicated. What this means is that the rate of mutation in functional DNA is independent of how much other DNA is being replicated. Excess DNA offers no protection from the spontaneous error rate of DNA replication.

THEME

Genomes & Junk DNA
However, the protection hypothesis may be applicable to other kinds of mutation such as those caused by chemicals or ionizing radiation. In multicellular organisms such as animals, fungi, and plants, this possible protection may prolong the lifetime of somatic cells or prevent them from becoming deregulated (e.g., cancer).

The idea is that excess DNA may shield the functional DNA from the effects of these mutagens but this would only work if the excess DNA was specifically organized so that it surrounded the functional DNA and provided physical shielding. There's no evidence that this is the case and, furthermore, it doesn't make much sense. The functional DNA in a nucleus is already shielded by lots of proteins, lipids and membranes so it's unlikely that a bit more DNA is going to make a difference.

Not only that, but some kinds of DNA damage caused by these mutagens will cause strand breakage. What does that mean? It means that the larger the genome the greater the chance that damage will occur. In other words, excess DNA leads to greater rates of mutation, not lower rates of mutation, for those types of mutagens. Ryan Gregory shows results from several studies during the 1970s that establish that fact.

I sympathize with Ryan's call for experimental support of the hypothesis but I'd also like to point out that not only does it not have direct evidence to back it up but it's not even theoretically feasible. It's just a bad hypothesis based largely on a misunderstanding of mutations and how they arise.

Also, the protection hypothesis doesn't pass The Onion Test which is one of the first requirements for an adaptive explanation of junk DNA.


On the Evolution of Homosexuality

 
A reader alerted me to a posting by Greta Christina on The Blowfish Blog.1 She discusses Why Did Gayness Evolve?.

This is not your ordinary posting on the topic. For one thing, she acknowledges that you can only discuss the evolution of homosexuality if there's a significant genetic component. She makes the assumption that there is a genetic component but it is not proven.

From that point on, her analysis of the possible reasons for evolving homosexuality is as good as it gets. Greta Christina avoids the obvious clichés and concentrates on real biology. The words "spandrels" is used a lot.

This is someone who understands evolution. Speaking of understanding evolution, in order to discuss whether homosexuality evolved you need to have a workable definition of evolution. My definition restricts evolution to heritable changes in a population and that's why the discussion of a possible genetic component is relevant.

Some people prefer a different definition of evolution—something like "descent with modification." I wonder how you can discuss the possible evolution of homosexuality using such a definition of evolution? Would it mean that the increased prevalence (and acceptance) of homosexual behavior in ancient societies was an example of evolution?


1. Thank-you Fred.

Thursday, December 10, 2009

Why Are Americans Religious?

 
One of the major questions in 21st century sociology is why are Americans so much more religious than citizens in other industrialized nations. The answer, if there is one, will help us understand why evolution is rejected by so many Americans.

Gregory S. Paul is a writer who has long been interested in this question. His latest contribution is published in the journal Evolutionary Psychology (Paul, 2009).

Paul examined the correlation between religiosity and the Successful Societies Scale (SSS). SSS measures things like crime rates, divorces, mortality rates etc. The United States (U) seems like an outlier compared to other countries.

Does belief in God cause a society to be dysfunctional or are less successful countries more likely to encourage religiosity? Or is there no obvious cause and effect behind this correlation?

You'll have to read the paper to see how Gregory Paul address these questions and how he rules out many possible explanations. I find his conclusion quite intriguing—I never thought of it this way.
Among the prosperous democracies all but the U.S. have adopted most or all of a set of pragmatic progressive governmental policies that have elevated these nation’s societal efficiency, success and security while reducing personal levels of stress and anxiety. These include reduced socioeconomic disparity and competition via targeted tax and welfare strategies, handgun control, anti-corporal punishment and anti-bullying policies, protection for women in abusive relationships, intensive sex education that emphasizes condom use, rehabilitative incarceration, increased leisure time that can be dedicated to family needs, and perhaps most importantly job security and universal health care that make it difficult for ordinary citizens to suffer catastrophic financial failure. Social ills are correspondingly suppressed. As a member of the 1st world the U.S. is an anomalous outlier not only in its religiosity, but in social, economic and political policies as well. Provided with comparatively low levels of government support and protection in favor of less restrained capitalism, members of the middle class are at serious risk of financial and personal ruin if they lose their job or private health insurance; around a million go bankrupt in a year, about half due in part to often overwhelming medical bills. The need to acquire wealth as a protective buffer encourages an intense competitive race to the top, which contributes to income inequality. The latter leaves a large cohort mired in poverty. Levels of societal pathology are correspondingly high. The evidence indicates that the modulation of capitalism via progressive policies is producing superior overall national circumstances compared to the more laissez-faire capitalism favored in the U.S.
       The relationship of religion to these patterns appears to be both passive and active. Starting with the passive, the middle class majorities of western Europe, Canada, Austro-Zealand and Japan apparently feel sufficiently secure in their lives that increasingly few citizens feel a need to seek the aid and protection of a supernatural creator, resulting in dramatic drops in religious belief and activity (Norris and Inglehart, 2004; Paul and Zuckerman, 2007; Zuckerman, 2008). With the implosion of the general religious belief, few subscribe to a fundamentalist world-view that provides the base for creationist opinion,. That there are no major 1st world exceptions to this pattern, and that a significant religious revival has yet to occur in a secular democracy, indicate that the socioeconomic security process of democratic secularization is highly effective even though it is an accidental side effect of progressive economic policies. The universality of the effect is further supported by Asian Japan experiencing the same basic secularization process as the EuroChristian heritage secular democracies. America’s high-risk circumstances, the strong variation in economic circumstances, and chronic competitiveness help elevate rates of social pathology, and strongly contribute to high levels of personal stress and anxiety. The majority of Americans are left feeling sufficiently insecure that they perceive a need to seek the aid and protection of a supernatural creator, boosting levels of religious opinion and participation. The nation’s good ratings in life satisfaction and happiness is compatible with a large segment of the population using religion to psychologically compensate for high levels of apprehension; America’s apparently high level mental illness (Bijl, 2003) may be in accord with this suggestion. The ultimate expression of this social phenomenon is the large minority who adhere to the evangelical Prosperity Christianity and Rapture cultures whose Bible-based world-view favors belief in the Genesis creation story. The results of this study are therefore compatible with and support the socioeconomic security hypothesis of democratic secularization.
Sue Blackmore is intrigued but skeptical [Are we better off without religion?]. She thinks this may be too simplistic and of course she's right. There's no one reason why America is lagging behind other nations in evolving a better society and there's no single explanation for its religiosity.

But I still think Paul's point is worth considering.


Paul, G.S. (2009) The Chronic Dependence of Popular Religiosity upon Dysfunctional Psychosociological Conditions. Evolutionary Psychology 7: 398-441. [PDF]

Friday, December 04, 2009

Quoting Bertrand Russell

 
Jason Rosenhouse has posted a quotation from Bertrand Russell [Quote for the Day]. Like Jason, I am a fan of the great man. Here's my quotation—it's from an essay written in 1940, shortly after Russell was declared unfit to teach at City College in New York.
A man or woman who is to hold a teaching post under the state should not be required to express majority opinions, though naturally a majority of teachers will do so. Uniformity in the opinions expressed by teachers is not only not to be sought but is, if possible, to be avoided, since diversity of opinion among preceptors is essential to any sound education. No man can pass as educated who had heard only one side on questions as to which the public is divided. One of the most important things to teach in the educational establishments of a democracy is the power of weighing arguments, and the open mind which is prepared in advance to accept whichever side appears the most reasonable. As soon as a censorship is imposed upon the opinions which teachers may avow, education ceases to serve this purpose and tends to produce, instead of a nation of men, a herd of fanatical bigots.
 

What Do These Things Have in Common?

 
What do these two images have in common? You'll have to read Ms. Sandwalk's blog to find out [One Month to go]. Next month will be very exciting. I'll be spending all of January in Belgium.




Defining Evolution in Anthropology Textbooks

Here's one of the most interesting articles in the current edition of Evolution: Education and Outreach.
White, J., Tollini, C.D., Collie, W.A., Strueber, M.B., Strueber, L.H., and Ward, J.W. (2009) Evolution and University-level Anthropology Textbooks: The “Missing Link”? Evo. Edu. Outreach 2:722–737 [doi: 10.1007/s12052-009-0176-6]

Abstract: Although studies analyzing the content of evolution curriculum usually focus on courses within the context of a biological sciences department or program, research must also address students and courses outside of the biological sciences. For example, using data solely from biological courses will not fully represent the scope of coverage of evolution in university education, as other fields, like anthropology, also utilize evolutionary principles. We analyzed the content of 31 university-level anthropology textbooks for the following: (1) presence of a definition of evolution in various sections of the textbooks, (2) accuracy and consistency of the definitions provided in the textbook sections, and (3) differences between textbooks for cultural and physical anthropology. Results of this study suggest that anthropology textbooks do not necessarily (1) provide a single definition of evolution or (2) provide an accurate, “baseline” definition of evolution when present. Additionally, substantive differences were observed between definitions provided in different sections within a single textbook, as well as between textbooks written for cultural anthropology and physical anthropology/archaeology courses. Given the inclusion of anthropology courses in general education curriculum at the university-level, we conclude that this situation may further exacerbate the misunderstanding of the basic tenets of evolution that university students have been repeatedly shown to demonstrate. We stress the role of the instructor in choosing textbooks that provide accurate information for students, as well as the responsibility they hold in providing a concise, accurate definition of evolution in social sciences courses.
The authors refer to an earlier study by Linhart (1997) who examined definitions of evolution in biology textbooks.
In our literature search, we were able to locate only one study that directly addressed the coverage of evolution in textbooks. Linhart (1997) focused on textbooks designed for one of the following six courses in the biological sciences: general biology (for majors and non-majors), evolution, genetics, paleontology, ecology, and systematics. He restricted his sample to 50 textbooks that had multiple editions and a sizable market share, and he located at least some of these textbooks using colleagues’ recommendations. He analyzed the content of the glossary entry for evolution in each textbook, as well as the material in any pages listed in an index entry for evolution, and compared these data against a definition of evolution he constructed after reviewing the literature:
Evolution is said to have occurred within a species, lineage, or population when measurable changes in various morphological, physiological, behavioral, or biochemical characteristics can be detected. These characteristics must be at least partly under genetic control. The genetic change(s) can occur as a
consequence of processes such as migration, mutation, genetic drift or bottleneck, natural selection, and nonrandom mating. Genetic changes within different populations of a species can lead to differences among lineages, and sometimes to the origin of new species...Evolution is not a synonym of natural selection. Nor is evolution a process that leads inevitably to increased or improved adaptation, or to greater reproductive success. Evolution does not imply a progressively closer fit between a population and its environment. Finally, evolution does not involve predictable or irrevocable changes from simple to more complex forms or toward some sort of perfection (Linhart 1997: 387).
While he found variation between the textbooks written for the six different courses in his sample, his findings indicated that the majority of all of the textbooks equated evolution with natural selection or adaptation and did not describe evolution in much detail. Linhart (1997) expressed much concern regarding the content of the definition of evolution in these textbooks, arguing that many students will have an inaccurate or incomplete view of evolution unless they are provided with additional material.
I agree with the problems that Linhart outlines and I agree that evolution needs to be defined as a process that involves genetic change and populations. It's very important that evolution should be defined in a way that allows for multiple mechanisms such as natural selection and random genetic drift.

Most of the biology textbooks I've read do an adequate job of defining evolution but I haven't covered as many textbooks as Linhart.

It's disappointing that biology textbooks and anthropology textbooks do such a poor job of defining—and presumably explaining—evolution. Is it any wonder that the general public is scientifically illiterate when we can't even get it right in the textbooks?


Linhart, Y. (1997) The teaching of evolution: we need to do better. Bioscience 47:385–91.

Evolution According to Niles Eldredge

 
I've read all of the books by Niles Eldredge. He's one of my favorite science authors [Good Science Writers: Niles Eldredge]. However, I've never really understood exactly what he means when he talks about evolution. He's not a molecular biologist or a geneticist but does he understand the basics of these disciplines? Does he think of evolution as a branch of population genetics or something else? Does he know about random genetic drift?

Some of these questions have been answered in an article that he co-authors with his son in the latest issue of Evolution: Education & Outreach. This is a journal dedicated to teaching evolution correctly. The article outlines a universal evolution curriculum for all grades from kindergarten to university [Lessons from EEO: Toward a Universal Evolutionary Curriculum].
Abstract We propose a human-centered evolutionary curriculum based around the three questions: Who am I? Where do I come from? How do I fit in? We base our curriculum on our experiences as an evolutionary biologist/ paleontologist (NE) and as a secondary level special education science teacher (GE)—and not least from our joint experience as co-editors-in-chief of this journal. Our proposed curriculum starts and ends with human biology and evolution, linking these themes with topics as diverse as the “tree of life” (systematics), anthropology, Charles Darwin, cultural evolution, ecology, developmental biology, molecular evolution/genetics, paleontology, and plate tectonics. The curriculum is “universal” as it is designed to be taught at all levels, K–16. The curriculum is flexible: “modules” may be expanded and contracted, reordered, or modified to fit specific grade level needs—and the requirements and interests of local curricula and teachers. We further propose that students utilize workbooks from online or printed sources to investigate the local answers to the general questions (e.g., “Who am I?”), while classroom instruction is focused on the larger scale issues outlined in the modules of our curriculum.
I don't like the idea of teaching evolution from a human-centered perspective. Our students are certainly used to thinking of biology only in terms of themselves, but isn't it our goal as educators to teach them that this is wrong?

It's the age-old question of whether the best way of teaching is to cater to student misconceptions or confront them.

A key part of any evolution curriculum is defining evolution. I prefer a scientific definition that allows us to distinguish evolution from other process that may look like evolution. The minimal definition is derived from population genetics and it allows us to recognize that different frequencies of blood groups in different human populations is evolution [What Is Evolution?].

Eldredge prefers a different definition in his evolutionary curriculum ...
What is “evolution?” Evolution is the testable, scientific idea that all species of life on Earth are descended from a common ancestor living billions of years ago since life first began on Earth. You can think of evolution as the history of life on Earth—or even as the fate of genetic information through time.

Module 3: What Is Evolution? How Do Humans Fit into the History of Life?

I've always taught that evolution is a process and that it's distinctly different from the history of life. It's like the difference between gravity and the history of our solar system. The formation of our solar system was a unique event that relied upon, and can be explained by, gravity and other general processes. Similarly, the history of life on Earth is a unique event. It can be explained by evolution and other processes but it's not the same as "evolution."

As far as I know, there are no evolutionary biology textbooks that define evolution as the history of life. The Eldredges are proposing a curriculum that's out of sync with most pedagogical approaches to evolution. Is this a better way to teach evolution? I don't think so.

Module 3 also covers the mechanisms of evolution. Adaptation and natural selection are mentioned but the authors go on to say that natural selection is not the only evolutionary process. The others are: speciation, punctuated equilibria, and mass extinctions.

I've always suspected that Niles Eldredge discounts random genetic drift as a legitimate process of evolution. This confirms my suspicion.

I'm very concerned about the content of this article and it's publication in a journal that's devoted to evolution education. If this is what the experts on evolution education are touting as the ideal curriculum then there are only two possible conclusions: (1) they aren't experts, or (2) I'm dead wrong about everything that I've been teaching.

I'm almost afraid to open up the comments on this posting for fear that (2) is the correct answer.



Wednesday, December 02, 2009

Comparison and Adaptation

 
As most of you know, Richard Dawkins is not a fan of the Spandrels paper by Gould and Lewontin [A Critique of the Adaptationist Programme]. A reader has alerted me to a comment that Richard Dawkins posted on Jerry Coyne's blog.

Dawkins said [I was there ...].
I was there (one of the speakers) at the London meeting of the Royal Society, where the Spandrels paper was first presented (by Gould; Lewontin didn’t come). Before Gould spoke, the talk by Clutton-Brock and Harvey substantially anticipated the Spandrels paper and undermined its central thesis. All of us were eager to hear how Gould would deal with Clutton-Brock and Harvey’s devastating critique of what they guessed (from previous publications) he would say. In the event, Gould totally ignored Clutton-Brock and Harvey, and gave his prepared paper, playing for horse laughs from the gallery, as if nothing had happened. It was the beginning of my disillusionment with Gould, whom I had previously respected. Please, if you read the Spandrels paper, look first at the Clutton-Brock and Harvey paper, in the same volume published by the Royal Society, 1979.
I had not heard of this paper by Clutton-Brock and Harvey and I'm not familiar with their work. Here's the reference and the abstract—it doesn't look to me like a devestating critique of Gould and Lewonton's paper.

Clutton-Brock, T.H. and Harvey, P.H. (1979) Comparison and Adaptation. Proc. R. Soc. Lond. B 205:547-565. [doi: 10.1098/rspb.1979.0084]
It has sometimes been suggested that the term adaptation should be reserved for differences with a known genetic basis. We argue that adaptation should be defined by its effects rather than by its causes as any difference between two phenotypic traits (or trait complexes) which increases the inclusive fitness of its carrier. This definition implies that some adaptations may arise by means other than natural selection. It is particularly important to bear this in mind when behavioural traits are considered. Critics of the 'adaptationist programme' have suggested that an important objection to many adaptive explanations is that they rely on ad-hoc arguments concerning the function of previously observed differences. We suggest that this is a less important problem (because evolutionary explanations generally claim some sort of generality and are therefore testable) than the difficulties arising from confounding variables. These are more widespread and more subtle than is generally appreciated. Not all differences between organisms are directly adapted to ecological variation. The form of particular traits usually constrains the form or value that other traits can take, presenting several obstacles to attempts to relate variation in morphological or behavioural characteristics directly to environmental differences. We describe some of the repercussions of differences in body size among vertebrates and ways in which these can be allowed for. In addition, a variety of evolutionary processes can produce non-adaptive differences between organisms. One way of distinguishing between these and adaptations is to investigate adaptive trends in phylogenetically different groups of species.


Vegetarian Nobel Laureates

I'm sure you've all been dying to know how many Nobel Laureates were vegetarians. Well, here's the answer. It was was on the back of a flyer received by one of the Skepchicks [An Appeal to Chickens and Other Logical Fallacies]. She's asking you to review the front part of the flyer to see how many logical fallacies you can identify.

It's interesting that only one Nobel Laureate won the Noble Prize for Physiology or Medicine. I guess the "logic" behind being a vegetarian isn't as obvious to biologists as it is to writers of fiction.




Name These Geneticists

This is a collection of "geneticists" from the latest issue of Genetics (November 2009). How many can you identify? The correct answers are here.





Tuesday, December 01, 2009

What Can't You Do in the House of Commons?

 
Almost anything goes in Ontario's House of Commons and debates can be rather lively. However, tradition (and House rules) state that you cannot accuse someone of lying. Here's what happens if you break that rule.



Ted Chudleigh is the Conservative MPP for Halton—a district that includes Oakville and Milton. He's ranting about a proposal to harmonize the GST and PST taxes.

Jennifer Smith lives in Milton and she's on the case. A little digging led her to this quotation from a speech by Ted Chudleigh in the House of Commons only 14 months ago [Ted Chudleigh on the HST: What a Difference a Year Makes].
Taxing businesses for their input costs is also a negative thing to do in an economy. It would be far better if we could find a way to harmonize the PST with the GST." (October 2, 2008 - Legislative Assembly Hansard)
Oh, dear. Is it possible that Mr. Chudleigh is a liar? Or is he just a hypocrite?


A Critique of the Adaptationist Programme


The Royal Society of Britain has opened access to a number of classic papers that have been published in Proceedings of the Royal Society. One of them is ...
Gould, S. J. and Lewontin, R.C. (1979) The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Programme. Proc. R. Soc. Lond. B 205:581-598. [doi: 10.1098/rspb.1979.0086]

Abstract: An adaptationist programme has dominated evolutionary thought in England and the United States during the past 40 years. It is based on faith in the power of natural selection as an optimizing agent. It proceeds by breaking an organism into unitary 'traits' and proposing an adaptive story for each considered separately. Trade-offs among competing selective demands exert the only brake upon perfection; non-optimality is thereby rendered as a result of adaptation as well. We criticize this approach and attempt to reassert a competing notion (long popular in continental Europe) that organisms must be analysed as integrated wholes, with Bauplane so constrained by phyletic heritage, pathways of development and general architecture that the constraints themselves become more interesting and more important in delimiting pathways of change than the selective force that may mediate change when it occurs. We fault the adaptationist programme for its failure to distinguish current utility from reasons for origin (male tyrannosaurs may have used their diminutive front legs to titillate female partners, but this will not explain why they got so small); for its unwillingness to consider alternatives to adaptive stories; for its reliance upon plausibility alone as a criterion for accepting speculative tales; and for its failure to consider adequately such competing themes as random fixation of alleles, production of non-adaptive structures by developmental correlation with selected features (allometry, pleiotropy, material compensation, mechanically forced correlation), the separability of adaptation and selection, multiple adaptive peaks, and current utility as an epiphenomenon of non-adaptive structures. We support Darwin's own pluralistic approach to identifying the agents of evolutionary change.
If you haven't read this paper by now then download it and read it carefully. It's the most important paper to read if you are interested in evolution.

Jerry Coyne agrees, "Read the rest; it’s certainly one of the most important papers in modern evolutionary biology." [It’s a spandrel (sort of . . .)!].

He also says,
This paper is famous because the authors were famous, because it’s very well written, but most of all because it posed a direct attack on the “Panglossian paradigm”: the view that sociobiology wants to explain all traits, particularly human behaviors, as the direct products of selection. This paper has been the subject of furious discussion and at least one book. In my view, the paper made some valid points but went overboard in its criticism of the adaptationist program, which, after all, has produced lots of insights about evolution. I knew Gould, who was on my thesis committee, and it always seemed like pulling teeth to get him to admit that natural selection was even a relatively important force in evolution. If pressed, he would, but Gould always preferred (perhaps for political reasons) to emphasize the limitations of selection. Lewontin was not nearly so extreme.
It's true that the adaptationists have produced some valuable insights when the problem they are examining is actually an adaptation. However, this isn't as significant as you might imagine. Think of it like this. Everything looks like a nail when you have a large hammer in your hand. The fact that some things actually turn out to be nails is no excuse for blindly whacking at everything that sticks up.

Gould and Lewontin advocated a pluralist position where many different kinds of explanations should be considered. They note that Darwin himself was not committed to natural selection as the only possible mechanism of evolution.
Since Darwin has attained sainthood (if not divinity) among evolutionary biologists, and since all sides invoke God's allegiance, Darwin has often been depicted as a radical selectionist at heart who invoked other mechanisms only in retreat, and only as a result of his age's own lamented ignorance about the mechanisms of heredity. This view is false. Although Darwin regarded selection as the most important of evolutionary mechanisms (as do we), no argument from opponents angered him more than the common attempt to caricature and trivialize his theory by stating that it relied exclusively upon natural selection. In the last edition of the Origin, he wrote (1872, p. 395):

"As my conclusions have lately been much misrepresented, and it has been stated that I attribute the modification of species exclusively to natural selection, I may be permitted to remark that in the first edition of this work, and subsequently, I placed in a most conspicuous position-namely at the close of the introduction-the following words: "I am convinced that natural selection has been the main, but not the exclusive means of modification." This has been of no avail. Great is the power of steady misinterpretation."




[Hat Tip: Pharyngula: Oldie moldies that are pretty darned fascinating]

On Determining the Structure of a Protein


Michael Clarkson is a biotech postdoc who blogs at Discount Thoughts. One of his recent thoughts is Don't look for "the" structure. He is referring to the fact that the crystal structure of a protein doesn't actually represent the only structure that the protein can adopt.

The figure shown here illustrates one of the problems with referring to the structure of a protein. This is a representation of an NMR structure of bovine ribonuclease A. It shows that various parts of the protein exist in several different conformations. The actual protein structure is a composite of all these structures in equilibrium with each other.

These conformation could be considered "breathing" and you may think they're not important. However, there are many cases where the conformations of a protein are quite different. We are familiar with allostery, where the conformation of a protein changes when it's bound to a ligand, but the are also examples where two very different structures exist in equilibrium in the absence of ligand.

Read his blog posting and keep in mind that proteins are dynamic structures and not static rigid crystals.



FOX News Pie Chart

 
One of Ms. Sandwalk's ancestors was William Playfair who invented the pie chart [Bar Graphs, Pie Charts, and Darwin]. That was in 1786.

FOX News has heard of the concept but they don't quite seem to have mastered the technique.




[Hat Tip: GrrlScientist]

The Cutest of all Invertebrates


Catalogue of Organisms features these cute little animals on "Taxon of the Week."

If you follow the link on that blog to a more detailed overview of the taxon you get a bonus—a description of why Christopher Taylor didn't make it to the International Conference of Arachnology in Brazil.